A bacteriophage (“phage”) is a virus that can specifically infect host bacteria and reproduces at the expense of the host bacteria. Shortly after their discovery, phages were proposed as a means to control pathogenic bacteria (d'Herelle, F., Bulletin of the New York Academy of Medicine 7, 329 (1931)); however, a poor understanding of the relationship between bacteria and phages led to frequent treatment failures, and the emergence of readily-available chemical antibiotics made phage therapy obsolete (Carlton, R. M., Archivum immunologiae et therapiae experimentalis 47, 267 (1999)). Presently, with the rise of drug-resistant bacteria and the sharp decline in antibiotic discovery (Fischbach, M. A. et al. Science 325, 1089 (2009)), phage therapy is regaining attention.
The limited range of bacterial cell hosts for a single type of phage has been a major challenge to the development and approval of clinical phage-based products. Traditionally, a phage “cocktail” was used to address this challenge (Sulakvelidze, A., et al. Antimicrobial agents and chemotherapy 45, 649 (2001)). Still, the desire to broaden the host range by adding different types of phages to a phage cocktail must be balanced with another challenge of producing and testing well-defined multi-component combinations for government regulatory approval.
Further still, creating phage-based therapeutics and diagnostics is limited by the difficulty of engineering phages. Phage genomes are often too large to be handled efficiently in vitro and reside for short periods of time in bacteria, which makes it difficult to modify the genomes during the phage reproductive cycle. Thus, phage genome engineering is classically performed with allele replacement methods whereby a piece of the phage genome is cloned into an appropriate bacterial vector, remodeled using classical molecular biology, and the bacterium containing the resulting construct is infected with the phage. The phage then recombines with the plasmid to acquire the desired mutations. This process, though, is inefficient because many phages degrade resident DNA upon entry and because the lack of phage selectable markers often make screening for acquired characteristics labor intensive. Moreover, there are very large stretches of phage DNA that harbor toxic functions and thus prevent their manipulation within bacteria.